Command Decisions
by InvisiblePrincess2002
Summary: The first in a series of small stories about Captain Janeway and the Doctor. AU. When Captain Janeway activates the Emergency Command Hologram and sends the Doctor to captain a medical ship on an errand of mercy, things go horribly wrong and the Doctor is forced to make a terrible decision that changes him forever.
1. Needing a Hug

**A/N: **This story is based on the television series, _Star Trek: Voyager,_ which as far as I know is the property of Paramount Pictures. **No infringement is intended. **This story is going to be the first in a series of small stories about the Captain and the Doctor. (These stories are basically my response to C/7, which I loathe for a number of reasons I won't get into here.)

**Chapter 1: Needing a Hug**

The Doctor felt truly sick inside as he stood stiff and erect in Captain Janeway's ready room, anxiously listening to her conversation with Premier Brill, one of the top leaders of the Nali race. It wasn't often that _Voyager's _egotistical, even arrogant Emergency Medical Hologram got a case of the shakes, but inside, he was definitely shaking now. The Doctor was not easily intimidated, but in these moments, he actually was terrified of the news Premier Brill was about to give to Captain Janeway.

Three weeks ago, _Voyager _had come into contact with a ship of kind, friendly aliens called the Nali, who were very tall and slim and bald with pointed ears. Captain Janeway and her (mostly) human crew quickly befriended the Nali, who were in the midst of a civil war with a highly aggressive cousin race of theirs called the Pirans. The Pirans had a fleet of ships scattered throughout the sector that had already gone to battle against _Voyager _a number of times, so obviously, Captain Janeway and her crew were quite relieved to run into the Nali and make a new ally in the Delta Quadrant deathtrap. The Nali ship, called the _Idora_, was a medical supply ship, and its crew was trying desperately hard to get back to their homeworld, Naliana Prime, because a viral disease had broken out amongst their soldiers and they badly needed medicine. Hundreds of Nali soldiers had already succumbed to the disease because it killed so quickly, and if the crew of the _Idora _didn't make it back to Naliana Prime in time, it was possible that thousands more would die. By the time the _Idora _crew came into contact with _Voyager, _their ship had already sustained heavy damage courtesy of a recent battle with the Pirans, and it was truly a miracle that the _Idora _and its crew were still in one piece. Since the _Idora _crew was on an errand of mercy, Captain Janeway decided it would be permissible in this case to bend the rules (meaning break the Prime Directive) and help out her new friends. Captain Janeway and her crew helped the Nali make repairs to their battered and broken ship, and then she made a command decision that would change both her life and the Doctor's life forever.

Most of the _Idora _crew were strictly medical personnel, and the remainder of the crew were pilots, engineers, ops officers, tactical officers, and of course a captain and a first officer, all of whom were there to keep the ship running while the doctors and nurses tended to injured soldiers on board. The _Idora_, like many other Nali medical ships, was basically a flying hospital that traveled to and from Naliana Prime and several other nearby Nali worlds, going wherever they were called to give necessary medical assistance to wounded and dying soldiers. In the _Idora's _last battle with the Pirans, the captain, the first officer, and all the engineers, pilots, and ops officers were killed and only medical personnel were left behind. And none of the medical personnel knew the first thing about running a starship or working on a bridge. Some of the doctors and nurses of the _Idora _crew had a little bit of piloting experience and were capable of flying a ship and of carrying out very basic evasive maneuvers in battle, but none of them came anywhere close to having the kind of expertise required to hold their own in battle against a Piran ship. To make matters worse, soon after Captain Janeway and her crew befriended the Nali aliens, a number of Piran ships arrived in the area and resumed their assault on _Voyager_, and Captain Janeway was left with no choice but to make an immediate and critical command decision. Thousands of lives were at stake on Naliana Prime, and it was essential that the _Idora _make it to its destination, but Captain Janeway had to ensure the safety of her own crew on _Voyager _as well. For obvious reasons, Captain Janeway needed all her crewmen at their battle stations so they could take on the Piran ships in combat, and she could spare almost no one. It was a hard call to make, but the Captain decided to activate the ECH, or Emergency Command Hologram, and send him over to captain the _Idora _and get the ship and its crew and medical supplies to Naliana Prime safely while she and the rest of the _Voyager _crew battled the Piran ships (and kept them too distracted to fire upon the _Idora_.)

Captain Janeway and her crew successfully managed to take the heat off of the Doctor, and thanks to her efforts, he was able to get the medical ship away from the battle. However, two days later, the Doctor ran into another Piran ship as he was trying desperately hard to get the _Idora _to Naliana Prime as soon as possible. Even with the extensive knowledge and tactical scenarios that had been programmed into the Doctor's ECH subroutines, there was really nothing he could do when the Piran ship fired on the _Idora _and quickly disabled it. It would take him days to repair the _Idora _and get it up and running again, and in the meantime, the ship was dead in the water. He sent out a distress call to any Nali ship in range, but unfortunately, the nearest Nali ship was twelve hours away at high warp. The Doctor hadn't been able to get in touch with _Voyager_, and while he had no doubt that the Captain would get the rest of the crew through the battle, he knew that they could still be too preoccupied with the other Piran ships to be able to come to his aid.

Soon after the Doctor sent out a distress call, the Piran ship began hailing him, so he opened a channel to the Piran captain. He immediately demanded to know if there were two doctors on board named Dr. Giala and Dr. Tress, who were sisters. The Doctor had already met and spoken with both ladies a number of times over the past few days and he knew they were onboard and he didn't lie to the Piran captain; he informed him that Dr. Giala and Dr. Tress were both members of the _Idora _crew. The Piran captain then told the Doctor all about a tragedy that had occurred fourteen years ago, before civil war had broken out between the Nali and the Pirans. Back when there had been peace between the two peoples, the Piran captain and his young son had been living on a Nali planet, and Dr. Giala and Dr. Tress had started their practice together in a building near his home. His son had gone on a field trip to a nearby world with the rest of his class one day and on their way back, their ship had a terrible accident. The Piran captain's son was badly injured, along with a number of other students, and many other students and teachers died in the crash that terrible day. Dr. Giala and Dr. Tress operated on his son and they did everything in their power to try and save him, but despite their best efforts, they weren't able to. Ever since then, the Piran captain yearned for revenge against the two women he blamed for the untimely death of his only child. Over the years, he had convinced himself that they hadn't done everything they could have done to save his son; that had his son been a Nali child, they probably would have done more for him. After the Piran captain told the Doctor about his son, he let him know that if he didn't immediately hand the doctors over to him, he would blow the _Idora _apart. The Doctor knew he didn't stand a chance against the Piran ship. He knew that if the Piran captain fired on the _Idora _just once more, it probably would be enough to destroy it. He also knew that thousands of lives were at stake on Naliana Prime. He knew he _had _to get the _Idora _there no matter what. And finally, he knew beyond the shadow of a doubt that if he gave in to the Piran captain's demand, he would be sending Dr. Giala and Dr. Tress to their deaths. He had to make a vital command decision, and he had only moments to make it. In panic and in pure, utter desperation, the Doctor did something that he never dreamed he would ever do in a million years. He did something that violated the very core of who he was. He beamed Dr. Giala and Dr. Tress over to the Piran ship.

As soon as the Piran captain saw that the two doctors were on board his ship, he immediately jumped to high warp and left the area. In a state of shock, the Doctor could think of nothing else to do except to begin making repairs on the _Idora, _and that's what he did. The Doctor worked hard and fast, and over the next two days, he managed to make all necessary repairs with the help of the Nali ship that had eventually come to his aid. Then the other Nali ship safely escorted the _Idora _back to Naliana Prime, where the Doctor and the rest of the _Idora's _medical crew quickly administered the badly needed medicine to all the Nali soldiers who had contracted the deadly virus, and thousands of lives were saved.

But now that he was standing in Captain Janeway's ready room days later, cold and clammy and nauseous and scared to death, he wasn't able to think about the overall success of his mission. He wasn't thinking about all the lives he and the rest of the _Idora _crew successfully saved. All he could think about was that split-second command decision he made in a moment when he was terrified and unable to see any other way out. All he could think about was the fate of the two innocent doctors he beamed over to a madman's ship without discussion. Without warning. The Doctor did _not _get frightened or intimidated easily, but now, he was so scared of what the Premier was saying to the Captain regarding the fate of the two doctors that he couldn't bring himself to listen to their conversation. He just completely zoned out while Captain Janeway and Premier Brill talked.

It wasn't until a few minutes later that the Doctor was brought back to reality by the gentle touch of his captain.

"Doctor," her voice softly called to him, bringing him back to the present moment, as she touched his arm.

"Forgive me, Captain," the Doctor said quietly.

"That's alright," Captain Janeway kindly whispered.

"What did the Premier tell you? Are Dr. Giala and Dr. Tress alright?"

After a long pause, the Captain finally locked her blue eyes with the Doctor's brown eyes and told him, "I'm so sorry, Doctor."

She didn't need to say anything further. The Doctor knew precisely what that meant. Dr. Giala and Dr. Tress were dead, and they were dead because of _him._ Because of _his _split-second, brutal command decision.

"Oh God," the Doctor gasped as he struggled to maintain his balance. After a few silent moments, he then told the Captain, "It's a good thing I'm a hologram. If I were flesh and blood, I'd probably be vomiting all over your ready room by now."

"Still Doctor, I think you need to sit down. Come on. Over here," the Captain said kindly while leading him over to the couch.

As soon as they sat down together, the Doctor looked at the Captain and whispered, "Thank you, Captain. You were right. I did need to sit down."

"It's understandable. The news you've just received is a terrible blow. It's enough to shock anyone, even a hologram."

"Dr. Giala and Dr. Tress were tending to a Nali soldier who was recovering in the _Idora _Sick Bay when I beamed them over to that maniac's ship. They weren't with me on the Bridge when I opened a channel and started talking to that captain. They weren't privy to our conversation. They were just going about their business, doing their jobs in Sick Bay, when I beamed them over. I didn't even have the decency to warn them about what I was going to do. I just did it."

"I've seen the logs from the _Idora, _and so have the Nali authorities. Doctor, we all know that there wasn't time for you to do anything else. You had no choice. Had you not acted quickly, Captain Bani would have blown the _Idora _apart. The _Idora _was the closest medical supply ship en route to Naliana Prime. It would have taken another ship far longer to arrive with the necessary medicine and supplies to help those soldiers. Thousands of lives were at stake and every moment counted. You didn't have time to take a poll. You didn't have time to try to formulate some kind of brilliant tactical plan to outwit him. You had only moments to make a decision. You did the only thing you could."

"I'm a doctor. I was programmed specifically with the Hippocratic Oath. I'm supposed to do no harm."

"In this situation, you weren't just a doctor. You were the _Idora's _acting captain. And as acting captain, you had to make a command decision. A heartbreaking command decision in the interest of the greater good. Sometimes, command decisions are difficult and painful. Brutally painful. But it comes with the territory of being a captain, or in your case, an Emergency Command Hologram."

The Doctor shook his head and laughed bitterly at himself, and then he said, "Funny. Back when I first came up with the idea of being an ECH, I had all these fantasies of the crew being incapacitated and me single-handedly taking on the Borg and being such a hero. But if this is what it really means to have command subroutines, to be in command of a starship, I want nothing to do with it."

"Doctor–" Captain Janeway began to say.

The Doctor quickly turned towards the Captain and said, "Captain, I request that you delete all of my command subroutines. I don't want to be an ECH anymore. After what I've done, I _never_ want to be in command of a starship again. I just want to go back to being a doctor, nothing more, nothing less."

"Request denied."

"But Captain–"

"No buts, Doctor. I understand how you feel, but like it or not, we need you as both a doctor and an ECH. We've needed you to function as an Emergency Command Hologram in the past, and we may need you to take over for us again in the future. And besides, making you an Emergency Command Hologram has given you valuable experiences that have caused you to learn and grow. I realize this recent experience has been incredibly painful for you, but I believe you'll grow from this as well. Growing can sometimes hurt very, very badly, but in the long-run, it's always worth it."

"It certainly doesn't seem that way now. Captain, I…_I killed two people,_" the Doctor gasped as a few stray tears fell from his eyes. "_I killed two people in cold blood. _How in the world am I supposed to live with that? How am I supposed to live with myself? How am I supposed to go on with my life?"

The Captain scooted a little closer to the Doctor on the couch, and then she lovingly brushed the tears out of his eyes with her fingers, and she told him honestly, "I'm not going to sugarcoat it. Even though we both know you did the only thing you could have done in an impossible situation, it's a cold, hard fact that this command decision you've made is something that's going to haunt you every day for the rest of your life. I wish I could sit here and tell you that it'll get better with time, but it won't. The pain will always be there. It'll always be a part of you. You never get over it. You just get on with it. You keep going regardless of how bad the pain is because you realize that at the end of the day, it's not about you. You have a whole ship full of people who need you, who are counting on you, and that's more important than whatever pain you're feeling."

After a long pause, the Doctor finally said, "That's not exactly comforting, Captain."

"No, I guess it isn't very comforting. But it's true. And as both your captain and your friend, I have to tell you the truth. Besides, we both know it wouldn't help you if I sat here and filled your head with lies."

"No, it wouldn't," the Doctor sighed. "Thank you, Captain. You've certainly given me a lot to think about."

"Of course," said Captain Janeway, and then she and the Doctor stood together. A moment later, she told him, "Listen. You've just been through a terribly traumatic experience and I think you could use some time off. Starting now, you're relieved of your duties for the next two weeks. Mr. Paris can cover for you in Sick Bay."

"I appreciate that. I think you're right. I think I do need some time off."

Captain Janeway nodded and placed a loving hand on the Doctor's shoulder. She then said, "Hang in there, Doctor. If you need to talk to someone, I'm always here for you."

"Thank you," the Doctor whispered. In those moments, there was a small part of him that actually yearned for a hug, for someone to just reach out and hold him, but he knew, of course, that it would be inappropriate to ask that of the Captain. Sure, Captain Janeway had been his friend for many years now, but she was his captain first and his friend second. And while he was friends with all of the other senior officers, he didn't feel comfortable enough with any of them to ask for the basic human touch that his heart was craving for now. Ironically, even though their ex-Borg crewman, Seven of Nine, often seemed to think more like a computer than a human being, the Doctor was closer to her than to anyone else and had he explained his need to be embraced now, she might have actually understood and obliged him. Now, though, it would be very awkward and inappropriate because a few weeks ago, Seven had begun dating _Voyager's _first officer, Commander Chakotay. Suddenly, it began to sink in during that moment that although he had plenty of friends aboard _Voyager_, he actually was painfully alone on a number of levels.

"Well, I guess I'll be going," the Doctor whispered, and then hesitantly, he began to walk out of the ready room.

"Doctor, wait," the Captain's voice called a couple of moments later, and he stopped and turned around. The Captain walked up to him then and said, "Doctor, I…"

"Yes, Captain?"

Clearly seeing how broken down he was, Captain Janeway wrapped her arms around the Doctor and gave him the hug his heart was yearning for. As the Doctor was holding onto her, he lost all control of his emotions and started crying. He cried and sobbed for several long minutes, and Captain Janeway didn't try to say anything to soothe him. She knew there were no magic words that could make any of this better. She just stood there and patiently held him in her warm embrace for the longest time and let him cry it all out. She knew that that was really the only thing she could do.


	2. The Doctor's Prayer

**A/N: **See Chapter 1 for Disclaimer.

**Chapter 2: The Doctor's Prayer**

Over the next month, the Doctor continued to struggle with himself inside. He'd gone through a similar struggle years before when both Ensign Harry Kim and Ensign Ahni Jetal were badly wounded by a mysterious alien while on an away mission. They were dying, and the Doctor only had enough time to treat one patient. In such circumstances, he was programmed to treat the patient who had the higher chance of survival. However, his program determined that the two ensigns had an equal chance of survival. Much like his situation aboard the _Idora_, time was of the essence, and he had to act fast. As difficult as it was, he had to choose one patient over the other before both of them were lost. He chose to treat Ensign Kim, the patient he was closer to, and his choice caused a conflict in his programming that he had to struggle to work through. The Doctor had needlessly blamed himself for Ensign Jetal's death, but as the years passed, he came to realize that it truly wasn't his fault that he'd ended up in that tragic situation. _He _never beamed over to another person's ship and fired a terrible weapon at two innocent people; the alien did that. And it wasn't the Doctor's fault that he was the only one on _Voyager _with enough medical expertise to perform the required surgery to save their lives and that a choice had to be made. Furthermore, as awful as it was to have to choose to treat one patient over another, in the end, it was a better outcome than simply doing nothing and losing both of them, and the Doctor eventually recognized that.

However, this situation was a whole other ballgame. The Doctor had no direct responsibility in the injuries that Ensign Kim and Ensign Jetal sustained and he was clearly not to blame for the fact that he had to choose one patient over the other. But this time, he played an active role in the ending of two innocent lives, and there was no escaping that knowledge. _He _made the decision for Dr. Giala and Dr. Tress to beam them over to a hostile Piran ship, captained by a madman who was hellbent on murdering them to get revenge. _He _knowingly sent them to their deaths without giving them any say in the matter. _He _became the judge, jury, and executioner of two kindhearted, brilliant women who still had many years of life ahead of them. _He _willfully made this ruthless decision to end their lives in cold blood. He knew he may as well have killed them both with his own hands, and it was destroying him on the inside. The Doctor didn't know who he was anymore.

During the four weeks that followed the Doctor's life-changing experience aboard the _Idora_, he came to the end of himself. He knew that he had a terrible stain on him that he couldn't clean up on his own. Ordinarily, the Doctor was the last one to even consider a belief in God, but these weren't ordinary times. He knew, down to the very depths of him, that he needed something that only a force outside of himself, greater than himself, could provide. He needed forgiveness. He needed the horrific thing he'd done to somehow be wiped clean.

He wasn't entirely sure what it was he was searching for when he began doing extensive research into all the various religious beliefs humanity had held over the centuries. He just knew that even though he had always looked down on people who believed in God in the past, seeing them as weak and primitive, now, there was something within him that desperately needed God to exist. But despite the fact that he was doing thorough research into humanity's various religions as well as the Bajoran and Klingon religions, he knew instinctively that he wasn't searching for religion. He was searching for something much greater than religion. He was searching for the Truth.

Finally, and reluctantly, he began searching in one last place: the Bible. After reading hundreds of texts that different religions considered sacred, he began studying Scripture. In human culture today, Christianity was typically viewed with contempt, and the Doctor was no exception. He too believed that Christians in the past were intolerant bigots and that Christianity's claim that Jesus Christ was the one and only way to God the Father and an eternity in heaven was horribly arrogant. But the more he studied the Bible, the more he came to realize that there was a stark difference between Christianity and all other religions. Every other religion he'd studied was, in a nutshell, man's attempts to earn his own eternal salvation. It was Christianity that acknowledged that no imperfect, sinful human being could ever attain God's standard of perfection on his own; that was all about nothing except pure, simple faith in the Son of God to achieve for man what man could never hope to achieve for himself. The Doctor knew earning his own salvation could never work for him because no amount of good deeds could ever undo his cruel command decision and restore the lives of the two innocent women he sent to their deaths. Only a perfect Being who was far more powerful than he was could find a way to heal the damage he had done and give him the forgiveness he needed so badly.

One evening at the end of his shift, the Doctor was in Holodeck Two running a program of a beach house in Hawaii. He stood on the front porch and watched the sun setting over the ocean. It was truly a gorgeous sight, but it just wasn't the same as the real thing. The Doctor had been on a number of worlds in the Delta Quadrant during away missions and he'd seen actual sunsets, and real, live sunsets seemed to be so much more magical than anything a holodeck could produce. He knew that if the beautiful and miraculous galaxy they'd been exploring for so long really had been created by Someone and had not been a random accident, then that Someone was terrifyingly powerful. Terrifyingly holy. Deserving of nothing but the deepest reverence and respect.

The Doctor eventually left the front porch and walked down to the beach. There were no other holographic characters hanging around in this program, so the Doctor was truly alone with his thoughts. After walking along the beach for a little while, finally, he looked up towards a God that he had once refused to believe in. That he now hoped existed because he knew he desperately needed Him.

The Doctor sighed then, and finally, he told the Lord, "I don't know what to say. I don't know where to begin. For all of my holographic existence, I've believed that it was primitive and foolish to believe in You. Maybe it still is; I don't know. But if You are there…if You even listen to holograms…then I really need Your help. If You do exist, I wouldn't blame You if You did find a way to eventually send my holo-matrix to hell. I deserve it after what I've done. But if You have room in Your heart for a murderous hologram, then please, have mercy on me, Jesus," he whispered as tears freely flowed from his eyes. "If You can go to the cross to make it possible for the sins of human beings to be forgiven, please let there be forgiveness for me, too. Please forgive me for killing Dr. Giala and Dr. Tress in cold blood. Please forgive me for every sinful thing I've ever done or ever will do. Help me. Please."

In the next moment, the Doctor literally felt Someone breathe life into him. And all of the sudden, he felt a heart, a human heart, beating in his chest. Then he heard a still, small whisper, telling him, "Your sins are forgiven."

Tears of overwhelming relief flowed from the Doctor's eyes for several minutes and he knew beyond a doubt that he'd been reborn. He knew that he wasn't imagining any of this; that it was real.

When the Doctor was finally able to talk again, he said, "Computer, give me a medical tricorder." Immediately, one appeared before his feet and he bent down and picked it up, and then he held it in front of himself and examined himself. When he saw the readings, he was stunned. The tricorder was picking up life-signs from the Doctor. He had a temperature, a blood pressure, a heartbeat. He was breathing real air into and out of his lungs. As astonishing as it was, the Doctor was now a human being.


End file.
